August 19, 2008

Our lab you must not enter

When I was fired from my first lab in college for the phosphine stinkup, no-one volunteered to have me so for awhile I had a bench and hood in the teaching labs. I was there alone, enthusiastic and without supervision. The glycidol story was mentioned already; I will describe two more memorable experiences:

Burning acrolein: We couldn’t buy things from Aldrich under communism and acrolein was unavailable from domestic supliers. Eventually I decided to make my own; there was an ancient lab procedure from glycerol by pyrolytic dehydration over KHSO4. (The yield is dreadful but we had a drum of glycerol in the stockroom). I did it on a grand scale and I ended up with about 0.5L of crude acrolein containing lots of water. To remove the water I got the idea of using magnesium perchlorate as a drying agent – we had a big bottle of that stuff on the shelf and I was reading somewhere that Mg(ClO4)2 was a potent desiccant comparable to P2O5 in its dehydrating proves. No wimpy sodium sulfate for me.

So I was spooning perchlorate into my acrolein and it kept dissolving – I ended up adding a whole lot of it and it was still dissolving and the mix was getting alarmingly hot and yellow. “Oh no, the perchlorate is all soluble and my acrolein is now polymerizing because of it, I will lose it all – quick, I must distill it all at once to rescue it!”. So I put the mix onto a heating mantle, added a distillation adapter and condenser and turned the heat on.

The hood sash was down and I was few meters away when a brilliant orange light from within the flask illuminated the lab and the entire hood turned black in an eyeblink. With a tremendous “wroooommrrr” that rattled the windows, the mix instantly burned away like a rocket engine and then the flame died out – before I realized what I have just done. The flask was still in one piece (only the condenser flew out) and a foot-high layer of soot was now filling the hood. The black tongues got painted on the wall behind the hood, emanating from the few places where the hood leaked. I turned around and saw a black cloud hanging by the ceiling and slowly settling down like a pillow. The entire lab got dusted with the greasy soot – a notebook lifted from the bench left a light rectangle behind…

It is inconcievable how much fluffy black dust can be produced from a half-liter of this mixture – I remember scooping out several buckets of soot that I had to smuggle out of the building. About six hours later (and a bottle of detergent) I was looking like a chimney sweep but the lab was all scrubbed clean and nobody found out about my perchlorate+acrolein jet propulsion experiment.

Milling KOH: I was about to reproduce some old-fashioned procedure that used a slurry of powdered KOH in toluene as a base. Now KOH is very hygroscopic – I tried to powder it with a mortar and pestle at first and the pellets were flying all over as I pounded on it while the stuff was melting into a puddle of lye. I realized the grinding had to be done very fast. Asking around, I found out that one faculty man owned a fancy electric grinder: The machine looked like a giant coffee-grinder on a blender; the container was made of heavy glass and the oversized motor had a beautiful aluminum casing.

“It’s the only power-grinder we have – You are not going to use it on anything corrosive, right?” – the owner asked. I assured him I wouldn’t.

The grinder worked amazingly well and in no time I had lots of free-flowing KOH dust (which I immediately bottled to keep it from getting soggy) – but I noticed as I was taking the grinder apart that I spilled some KOH dust onto the motor casing and the aluminum was getting pitted by the hydroxide. More worryingly still it looked like the caustic dust has gotten into the electric motor itself through the vent holes in the casing. It gotta be cleaned promptly.

I was not familiar with the Mr. Bean skit character back then, but with the same kind of single-mindedness I proceeded to wash up the motor casing in the sink. I was not careful and some water splashed through the vent holes – and since the KOH dust got in there and the electric motor was already wet, I decided that the motor deserved a proper rinse as well – I would dry it afterwards. So I had the water flowing in and through the motor.

The owner of the grinder dropped by later that afternoon to find out how it worked (and if I was ready to return it). I said I needed to clean it up a bit more – the motor was still very soggy and I prefered not having to explain how it got that way.

Wet glassware dries pretty fast when rinsed with acetone. Being in hurry I reached for a squeeze-bottle and washed the motor with acetone too – and surprise – the acetone coming out from the motor was dark brown and smelling just like shellac resin that is used to insulate the fine copper winding in electric motors…

I was horrified, I realized I just ruined it completely and I better try to cover it up. I dried the motor with a heat gun and assembled the grinder. I gave it a good final polish and then I waited patiently until I saw its owner walking away from his lab – and then I sneaked in and put the grinder back in the cabinet as if nothing bad was done to it (I turned the pitted aluminum part away from the sight). Just as I was closing the door the owner returned. “Thank you – it worked great. I put your grinder back and it’s all clean now…”

But the luck was not with me. “OK – let me see if it still works” the guy says – and he takes this thing out and plugs it in the wall. A loud bang and a green-and-white lightning, the sparks flying all across the room and rolling on the floor before gradually dying out like embers. (I saw a street transformer once, blowing up like that but from a safer distance). We were standing there in silence for few long seconds – the only sound was the “klip-klop-klop” from the hallway as the circuit breakers gave up one by one and plunged the chemistry building into darkness.
The faculty guy then turns to me and says: “Thank you. Don’t hesitate if you need my help again.”

I tried to grind KOH like that once. I powdered it up in the blender and took off the lid, only to inhale a breath of KOH dust. That really sucked and with most lab accidents like this, I realize how foolish I was.

Diluted – I think KOH powder is not much used nowadays, precisely because it is so unpleasant to work with. This must have been a really ancient procedure.

But inorganics getting soggy is a common problem – I wouldn’t try to powder a moderately hygroscopic material like Cs2CO3 here in southern Florida. We have difficulty with just weighing stuff, like NaH in oil. I sometimes postpone setting up sensitive experiments – especially those done on a miligram scale – when it’s pouring outside and there is a chance of the rain coming to end later. You probably have this kind of problem there also – the high humidity that makes the glasses fog-up when stepping out from the air-conditioned building or a car…

That’s precisely why Grignard reactions NEVER work in Singapore. It’s too humid. Even when we use an N2 filled glove box, you’d have to have pretty green fingers to get it to work. But because it’s so humid here, women don’t get fine lines on our faces until we are really old, like 40. LOL!

In Singapore, I’ve succesfully done Grignards and I have friends who routinely use it to prepare Suzuki substrates… so I don’t think that’s much of a problem. If we can get BuLi to work here, I don’t see how Grignards can fail.

Did you check your solvent? Ether can dissolve a fair amount of water. Did you clean the Mg ribbon? Crush or stir it around a bit?

BuLi is not such a deal – people dont make it from Li metal anymore, you get it in a bottle and if there is not too much sediment you dont even need to titrate it for most applications. With Grignards the main problem is how to start the reaction. Taking flasks hot from oven and flushing them with dry Ar, transferring ether directly from stil by canula etc is the way to go – but it is not as easy for a freshman to do it correctly. I remember my own difficulties with a humid summer in Boston, trying to make anhydrous copper(II)-Box catalysts. (Later it turned out that the moisture improved the reaction – the hydrated catalyst was much milder on my substrates)

To make Grignards from scratch – Polish the Mg ribbon off with sandpaper, stir it like there’s no tomorrow, and heat it just slightly (not any more than 35 C for Et2O) with a water bath and use a condenser, of course – that usually does the trick for me. and oh, don’t forget to put a couple of I2 crystal to show the rxn is starting.

Can you grind KOH in hexanes? I have never done that but we used to weigh NaH in hexanes (to rinse off the oil) and cannula off the hexanes after. I assume you may be able to do something like that for KOH to keep the water out – and you can always suck out the hexanes or blow it off with N2, assuming a little residual hexanes does not affect the reaction.

To grind KOH heat it and the mortar and the pestle to 80-100 C (no higher; 80% KOH pastilles melt), then go for it wearing insulated gloves, a face mask, and safety googles. Big mortar and pestle is good. Work fast, be very neat. Tared PE zip-lock bag for storage. Bag the bag.

hey, i work in the pharma industry n I’ve been reading some of your posts..quite interesting. So what’s ur real identity? name/profession/country? And why did you choose milkshake as a name?

[ I am a synthetic organic chemist doing medchem research. A chemistry-motivated reader can find my office phone and home address in about 20 seconds (and I prefer to keep my semi-anonymity for the rest of the visitors). I chose this nick because it’s memorable – please think of me as the Clockwork Orange character. And you know quite well that I served time under your current employer and that I wrote a post about the experience few months ago – “Such, such were the joys”. Cheers, Milkshake ]

Uncle: That’s a neat trick – I never heard of it and haven’t thought of it either. (I was using oven-hot bottles before, to transfer and store super hygroscopic solids – but not a hot mortar and pestle.)

I just always thought of typical toolbox items (hammer, screw drivers, plyers) as part of normal lab utensils. So people don’t use brute force anymore to powder KOH or other solids? I used to always wrap in Paper towel or Heavy Filter Paper then pound with vigor with side of hammer. Unfold and remove bigger chunks with twizzers or just sieve. You can put it in a heavy Ziplock bag to contain or protect from moisture although more cumbersome. Afterwards dry powder under Hi-vac then store under N2 gives a stock supply and if it flows then still good to use. Yeah you can do all in glovebox/bag but how often does it need to be so dry?

Also agree with andrew that if Grignard initiation a problem likely need to pound the Mg a bit to expose fresh surface. Taking Mg through a heat up/cool down cycle can help encourage reaction.

also add a wrench (for gas tank regulators) and a hand-saw: very useful – when we started in a temporary rented lab we needed a wooden backing contraptions just to attach the stainless steel drying racks above the sinks – so I went to Home Depot, bought some wooden beams and screws and epoxy and did the carpentry work; the saw then came useful later when amputating legs on ridiculously tall lab tripod stool, and when making a large-scale cooling bath container from a plastic drum that our bulk bicarb came in

Our NMR guy uses a leftover piece of wooden stick (that I bought to fix the glassware racks). He would crawl under the magnet, take the probe out and poke on a sample with the stick from the bottom if a sample gets stuck in the magnet (like when somebody’s NMR tube cap falls off in the magnet and blocks the spiner ejection). This low-tech approach is vastly preferable to disassembling the magnet core tube – which we unfortunately had to do recently also.

Another neat trick for “anhydrous KOH”, although it may not work in every case is to pre-stir a measured amount of water with a slight molar excess KOtBu. Supposedly good for getting dehydrated KOH in situ for ester or amide hydrolysis (although it didn’t work for me on a very bulky malonate diester…)

Don’t want to change the subject for too long, just wondering if a relatively new bottle (opened within the last year, kept in freezer) of methyl acrylate should be distilled prior to use in a Stork enamine alkylation. I’ve never used this reagent before. Thanks!

Few weeks ago, we had an accident due to KOH. One of my labmate was making KOH solution in 500 ml beaker on the bench. The KOH soln (beaker)slipped from her hand(she did not care that her hand palm got KOH soln) and spilled on the bench and shelves. it was really difficult to clean . it looked like cleaned one but the slippery surface was remained for many days.

I have never done enamine addition to acrylate myself, I only saw it in a book. I would use acrylate straight from the bottle – my experience with Aldrich Me-acrylate is that it stores very well if kept in a dark cabinet, even at room temperature. If you want to distill it, add few crystals of BHT or hydroquinone to the receiving flask (I heard stories from a factory where they make acrylates – digging out ton-quantity of half-polymerized sticky goo from the system is not very funny, it happened to them repeatedly when they started there).

Also, please Me-acryalte has extremely strong and tiresome rum-and-garlic-and-mushroom odor, use it in hood and do the workup and evaporation at night or early morning, when not too many people are around – because they will all come to you and complain! Make sure to clean up the rotovap afterwards. Acrylates are quite unhealthy.

Cat Herder if you take an 1HNMR you can get an idea of how good your MeAcrylate is (multiMe peaks bad? I can’t remember exactly). I have gotten crap stuff from Aldrich which needed to distill prior to first use but is a simple distillation. Although polymerization possible I wouldn’t use the inhibitors suggested and just use ice cooled collection flask and then keep in frig under N2 thus good for months (rubber septum OK for short time but will deterioate/blacken over time). Keep material in dark (Al foil) may help. I mainly did radical rxns (thus didn’t want inhibitors) although ran a few Michals (do not know if inhibitors matter there). Milkshake is correct about the powerfull smell so do keep/wash everything in hood, even best to put rot vap in hood if necessary. I had a base bath in my hood to clean/soak glassware but people normally could tell when I used arcylates.

Any advise for low-melting reagents like DCC? Those that the manufacturer charged into the bottle molten, leaving you with a singular rock which can’t be removed without any considerable effort?

Sick of chipping at the chunk with first a spatula, then pounding away with a half-inch aluminium rod, I called Aldrich to complain of a a bottle of 4-chlorobenzaldehyde, demanding that they replace it with another bottle of free flowing powder.

This was the second bottle. I smashed the first bottle with the gas regulator-wrench, chopped it up with the same wrench, and rolled it into the desired fine powder with a Schott bottle.

Aldrich only suggested that I warm it up and pour it out. It works, but it’s stupid ‘coz I want to weigh it as a powder, not draw it as a liquid (and have it freeze, jamming my Pasteur pipette)…

This is most annoying, I had to put many of these low melting solids onto my running oil pump to warm up.

But DCC can be handled as a solid and there is a trick to crushing it: DCC is waxy soft (=softer than warm ice) if compressed slowly but very brittle when pushed fast. I always wear good gloves and goggles because DCC is such an insidious allergen, and I would take a heavy-duty large spatula, push the flat sharp end into the block of DCC in the bottle gently, about half-inch deep, then pull the spatula out, leaving a slit. Then I would press in the spatula gently about 1/4 inch apart in parallel with the slit, then wiggle/twist the spatula a little so that the chunk in between the two slids breaks off controlably, wihthout bits flying all over. Then repeat as needed; it actually gets easier once you make a decent gash in the block. No use to pound on it – it flies when hammered. (And if you are not sensitive to DCC-induced rash, your colleague next hood might be).

Some companies like Advanced Chemtech (now available through VWR) actually sell DCC pre-crushed in manageable chunks and packed in a plastic bottle – one smack with the plastic bottle on the bench and the chunks are free-flowing again.

CMC and Milkshake. Reaction worked as well as anticipated (i.e. ~50% yield), so I guess I didn’t need to distill the Me acrylate. Thanks for the warning about the stench, you guys weren’t exaggerating. However, I did it yesterday so no one was around. Thanks for all your help!

In my former lab, with things like 4-chlorobenzaldehyde, we basically put the (glass) bottle inside 2 ziploc bags and smashed the bottle fairly cleanly with a wrench. Then, took the glass out, closed the Ziploc bag and smashed the solid into small manageable pieces. I assume that’d work for a lot of things. Oh, and those super-old bottles of hygroscopic solids like KF…!

I always used the stiff spatula and hammer approach with small hits, along with eventually slight heating inside the rotavap bath at 40°C.
Bottle must be alive to contain the rest of the material ! It is not to blame about the phisical characteristics of the solid…

I did lots of Baylis-Hillman reactions with Me-acrylate at one time. The problem is that it is hard to keep the smell to yourself. Other acrylates (ethyl, benzyl) are actually worse because they have a strong mushroom smell.

I used a biology incubator once, to run the slow Baylis-Hillman reactions in capped vials for days at 40C – but one of the vials must have leaked and it killed all cells in that incubator, the biologists were rather pissed about it – as you can imagine… It shows acrylate is rather unhealthy.

When you work with methacrylates and especially with acrylates you get a color index of your nails beforehand. When they start turning bluish it is time to leave for the day. Nasty for inhalation and contact.

Finely powdered KOH in pyridine can be a spectacular base for doing methyl ketone-ester condensations to 1,3-diketones around 40-50 C. Product potassium salt precipitates out. Had the next step in the synthesis cooperated it would have been even better.

Since you’re talking about mushrooms, ethanedithiol smells intensely of that. No amount of hand-washing with detergent and bleach will rid your fingers of that smell too (no, I don’t usually wear gloves)…

when one crack-opens a safe or ATM machine ineptly, a capsule with a strong blue dye gets triggered and explodes inside and everything is stained, the dye is particularly hard to wash off.

It turns out they had the same system in former USSR except that their stain was bright orange-yellow. My russian boss at previous company used to work with merrocyanine dyes that were intensely yellow-orange, and he was not wearing gloves. One day, the “milicioner” patrols were on look-out for a bank-robber, and they saw the poor chemist in the Kiev subway with his orange hands. He got arrested, got a softening treatment with a batton on the spot and then was interrogated for two days without sleep by the KGB – and he confessed everything 🙂

I’m sure it’s possible to coerce one into solubility…tack on enough isobutyls and you can probably spincast a brick. 😉
(Then there’s that issue of spectral coverage…with a lot of phthalocyanines there’s one band with crazy extinction and then not much else. Just a generalization–pretty sure there are exceptions!)

Fortunately we have a whole set of tools in our workgroup. I think I have used quite a few of them already during my time there.
I can understand that grinding KOH in a very humid atmosphere isn’t easy, but I did at least manage to grind it like 5 gram wise in the mortar without problems(I am in Berlin, Germany, so no, we don’t have high humidity). In the 5 minutes or so it took me to transfer it into my flask it didn’t go liquid either, and i didn’t need 100% dry KOH anyway for the reactions I did.

I like your blog, Milkshake! A lot of useful tips and tricks. Just wanted to contribute the one concerning alkali grinding.
Cover the reqired quantity of alkali with dry DMSO and heat the mixture until solid turns to liquid, then stirr vigorously and cool slowly until fine suspension forms. Works great especially if you can carry out your reaction in DMSO.
Alternatively, add dropwise a saturated aqueous alkali solution to at least 3 volumes of THF or dioxane with vigorous stirring.
Kindest chemical regards. 😉

I was doing an alkylation in my undergraduate project that failed under most conditions, started to yield about 5-12% with NaH in certain solvents. Then I tried powdered KOH in DMSO (both anhydrous) at room temperature, supposedly conditions Steve Ley “invented” in his own undergraduate studies, and my yields shot up to 57% which I was more than happy to run with. I was actually turned onto these conditions by a senior in my lab who had solved a stubborn alkylation of her own by stumbling on those conditions. So it remains the one purpose that I will occasionally find myself grinding KOH in our relatively humid climate, as I’ve got a soft spot for those alkylation conditions. Grinding as quickly as possible with a hot mortar and pestle is the only way to go, and the chunky bits can always be cast aside later once it’s in a nice dry vial.

Actually the best way to go about it is to take a cheap kitchen blender with a glass container, buy Fisher technical KOH “flakes” (not pellets) and dry mill the flakes into powder using the blender. It works like a charm in humid Florida. For extra kick I recommend adding 18-crown-6, 10 – 20 mol% in toluene or benzene but in DMSO having crown around is probably unnecessary. (The DMSO + KOH condition is particularly nice for N-alkylation of indole, where C alkylation often competes.)